ArticleBMC bioinformatics2008
Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
6 citing papers in PubMed, 7 citations in OpenAlex.
- GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.PLoS genetics · 2014Article
- High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast.Genome research · 2013Article
- Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae.Cell · 2012Article
- Novel features of ARS selection in budding yeast Lachancea kluyveri.BMC genomics · 2011Article
- A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.PLoS genetics · 2010Article
- Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances.PLoS computational biology · 2010Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundIn analyzing the stability of DNA replication origins in Saccharomyces cerevisiae we faced the question whether one set of sequences is significantly enriched in the number and/or the quality of the matches of a particular position weight matrix relative to another set.
resultsWe present SADMAMA, a computational solution to a address this problem. SADMAMA implements two types of statistical tests to answer this question: one type is based on simplified models, while the other relies on bootstrapping, and as such might be preferable to users who are averse to such models. The bootstrap approach incorporates a novel "site-protected" resampling procedure which solves a problem we identify with naive resampling.
conclusionSADMAMA's utility is demonstrated here by offering a plausible explanation to the differential ARS activity observed in our previous mcm1-1 mutant experiments 1, by suggesting the relevance of multiple weak ACS matches to efficient replication origin function in Saccharomyces cerevisiae, and by suggesting an explanation to the observed negative effect FKH2 has on chromatin silencing 2. SADMAMA is available for download from http://www.cs.cornell.edu/~keich/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.